Force first revision xref to not have subsections

DEVSIX-1428

Author: Benoit Lagae

kernel/src/main/java/com/itextpdf/kernel/pdf/PdfDocument.java

@@ -800,12 +800,14 @@ public void close() {
                     flushFonts();
                     writer.flushWaitingObjects();
                     // flush unused objects
-                    if (isFlushUnusedObjects()) {
-                        for (int i = 0; i < xref.size(); i++) {
-                            PdfIndirectReference indirectReference = xref.get(i);
-                            if (!indirectReference.isFree() && !indirectReference.checkState(PdfObject.FLUSHED)) {
+                    for (int i = 0; i < xref.size(); i++) {
+                        PdfIndirectReference indirectReference = xref.get(i);
+                        if (indirectReference != null && !indirectReference.isFree() && !indirectReference.checkState(PdfObject.FLUSHED)) {
+                            if (isFlushUnusedObjects()) {
                                 PdfObject object = indirectReference.getRefersTo();
                                 object.flush();
+                            } else {
+                                indirectReference.setFree();
                             }
                         }
                     }

kernel/src/main/java/com/itextpdf/kernel/pdf/PdfXrefTable.java

@@ -151,9 +151,7 @@ protected void freeReference(PdfIndirectReference reference) {
             if (reference.getGenNumber() < MAX_GENERATION) {
                 freeReferences.add(reference.getObjNumber());
                 ensureCount(Math.max(this.count, reference.getObjNumber()));
-                xref[reference.getObjNumber()] = null;
             }
-
         }
     }
 
@@ -170,15 +168,9 @@ protected void setCapacity(int capacity) {
      */
     protected void writeXrefTableAndTrailer(PdfDocument document, PdfObject fileId, PdfObject crypto) throws IOException {
         PdfWriter writer = document.getWriter();
-        if (document.isAppendMode()) {
-            // Increment generation number for all freed references.
-            for (Integer objNr : freeReferences) {
-                xref[(int) objNr].genNr++;
-            }
-        } else {
-            for (Integer objNr : freeReferences) {
-                xref[(int) objNr] = null;
-            }
+        // Increment generation number for all freed references.
+        for (Integer objNr : freeReferences) {
+            xref[(int) objNr].genNr++;
         }
         freeReferences.clear();
 
@@ -205,9 +197,7 @@ protected void writeXrefTableAndTrailer(PdfDocument document, PdfObject fileId,
         for (int i = 1; i < size(); i++) {
             PdfIndirectReference reference = xref[i];
             if (reference != null) {
-                if ((document.properties.appendMode && !reference.checkState(PdfObject.MODIFIED)) ||
-                        (reference.isFree() && reference.getGenNumber() == 0) ||
-                        (!reference.checkState(PdfObject.FLUSHED))) {
+                if (document.properties.appendMode && !reference.checkState(PdfObject.MODIFIED)) {
                     reference = null;
                 }
             }